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I dont get the output file to "gatk CollectAlignmentSummaryMetrics" that use to get alignment and insert size metrics in variant calling process

score 63 · Answer 1 · 2024-01-16T17:54:13.207000

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I dont get the output file to "gatk CollectAlignmentSummaryMetrics" that use to get alignment and insert size metrics in variant calling process

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TechQA.

List Question

I dont get the output file to "gatk CollectAlignmentSummaryMetrics" that use to get alignment and insert size metrics in variant calling process

Troubleshooting GATK Pipeline Error in AWS ParallelCluster Environment and Spark

Parsing FORMAT and sample value fields from VCF file

base recalibrator --known-sites argument does not work

GATK4 is rejecting my RGSM when using AddOrReplaceReadgroups

GATK Variant Filtration file Anopheles gambiae s.s

New: Fatal error compiling: java.lang.NoClassDefFoundError: com/sun/tools/javac/main/OptionName: com.sun.tools.javac.main.OptionName

BaseRecalibration by GATK

How do I use this python function within the params section of my Snakemake rule?

GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

Snakemake integrate the multiple command lines in a rule

Snakemake first genotype of a vcf file as wildcard in output

How to run ensembl-vep in conda

Error running gatk HaplotypeCaller with allele specific annotations

Snakemake: create multiple wildcards for the same argument

Combine a directory of GVCF files with gatk CombineGVCFs

gatk VariantRecalibrator positional argument error

What does 'NEGATIVE_TRAIN_SITE' in VQSR mean?

snakemake multiple parameters for multiple input and single output in snakemake. ConbineGVCFs gatk problem

Running docker from bash script

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